On 3/21/13 10:20 PM, 라지브간디 wrote:
Dear gmx users,
I am MD simulation for heme ligated protein where i given all bond and angle,
dihedral information in topology file created by pd2gmx ( gromos43a1).
However, i do not know how to interpret the proper and improper dihedrals in
topology file? I have looked over the .rtp file and found that gromos mentioned
like
example:
[ impropers ]
; ai aj ak al gromos type
C2 N1 N3 NA2 gi_1
NA2 HA21 HA22 C2 gi_1
N3 C2 C4 HA3 gi_1
But the the parameter I use from literature where its in charmm and amber
format as they mentioned the torsions like following way.
Improper
CPB-X-X-CR1E 90.0 0.0
CC - X-X-NB 18.3 0.0
...............etc
How do i use this improper to utilize in gromos?
Every force field has small differences in format. Look at ffbonded.itp for
43A1 and you will see #define statements that correspond to bonds (gb_*), angles
(ga_*), etc. Those macros just mean "substitute this information here." It's
shorthand. So either you can introduce a new definition in ffbonded.itp or just
type the parameters in manually according to the format specified in the manual.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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